Romancing the Prehistoric

I was – note the past tense – going to write a post about re-entry after Covid-19 vaccination and how awesome it was to give my younger daughter a hug after over a year, but then I saw this story from Science magazine and could not resist.

Did you ever wish you could see a living dinosaur? I sure did! (I still do…but from a safe distance.) As a child I loved movies with stop-action animation of dinosaurs, like the original King Kong or the Ray Harryhausen movie, The Valley of Gwangi. In high school I wrote a short novel about two teenagers and their horses who discover a hidden valley where dinosaurs still roam. Jurassic Park and its sequels blew me away, the movies even more so than the novels. The novels were longer on explanation, the movies far more powerful in vividness. The moment when Alan Grant, upon learning that Professor Hammond has created a T. rex and almost faints,  that’s how I would have felt. Great acting and directing aside, these books and films spoke to a universal or near-universal human longing to see amazing charismatic animals from the distant past.

The earlier stories, at least the ones I read and watched, made no effort at a scientific basis for the present-day existence of prehistoric animals. It was all “Land That Time Forgot” hand-waving. Crichton took a different tack: dinosaurs did not persist in some undiscovered corner of or beneath the Earth: humans re-created them using DNA preserved in amber. We’ve been able to recover DNA from Pleistocene mammals, but never anything as old as 65 million years. Many scientists doubt that DNA could survive that long, no matter how preserved. When an animal dies, its DNA begins to decay. A 2012 study on moa bones showed that genetic material deteriorates at such a rate that it halves itself every 521 years. This speed would mean paleontologists can only hope to recover recognizable DNA sequences the past 6.8 million years. In 2020, Chinese Academy of Sciences paleontologist Alida Bailleul and her colleagues proposed they had found a chemical signature suggestive of DNA in a 70 million year old baby hadrosaur fossil. If confirmed, this material would be so degraded into components, not sequences. It’s also possible the chemical signature was that of bacteria, not the dinosaur itself.

The Siberian permafrost that has yielded mammoth DNA is about 2.6 million years old, but freezing turns out to be a pretty good preservative of DNA. Scientists have now been able to sequence DNA from extinct mammoths 1.2 million years ago. That’s a world record. The previous record, in 2013, was from a 750,000-year-old horse. The new study includes DNA from three species of mammoth from three time periods (1.2 million, 1 million, and 700,000 years ago) and there are all kinds of reasons to be excited about it, not just the age but the evolutionary relationships and a previously unknown type.

Which brings us to the question we’re all asking: Once we’ve sequenced this DNA, whether from mammoths, saber-toothed cats, ground sloths, or whatever – what do we do with it? What we can do now is better understand the evolution and relationships of these amazing animals. What popular media want, however, is to use the material to create living extinct species. The process of de-extinction can proceed either by cloning – taking material from a recently extinct species and replicating it – or by using ancient, fragmentary DNA. We’ve got a long way to go with either technique. Many extinct species lack contemporary surrogates to carry the artificially created embryos to term. For others, suitable habitat no longer exists (really? Where would you turn a giant ground sloth loose? A saber-toothed cat? Or would these animals exist only in the unnatural environment of zoos?) Back in 2009, Spanish scientists cloned a newly extinct Pyrenean ibex, although the clone died within a few hours of birth.

There are, however, a few good candidates for which possibly viable DNA sources exist. Species like the passenger pigeon and Carolina parakeet might fare well, given the human responsibility for their disappearance, although they might turn out to be temporally invasive species. Continue reading “Romancing the Prehistoric”

Beware Fake Science News!

Barbara McClintock, geneticist

Science news articles abound, everything from the results of carefully designed peer-reviewed research studies to fear-based rumors and anti-science biased conspiracy theories. How are we to discern which are reliable, which are hype based on misinterpretation, flawed studies, and the like, and which are clickbait nonsense?

The first thing I do is look at the source. Mediabiasfactcheck and other sites provide information as to the right-left biases and factual accuracy of a given source, although not of a particular story. Science Based Medicine is also helpful. I’ve been known to search under “Is Dr. So-and-So a quack?” and get useful answers.

I also check my own reactions: Is this too good to be true? Is it at odds with what I understand about science (my academic background is biology and health sciences)? Have I seen an article in a trusted source (such as the newsletter from Center for Science in the Public Interest) debunking this or similar claims? I’ve been also known to check with friends with special expertise in the field.

The Conversation offers some guidelines on assessing the quackery scale of science new stories. Their suggestions:

1. Has the story undergone peer review?

Scientists rely on journal papers to share their scientific results. They let the world see what research has been done, and how.

Once researchers are confident of their results, they write up a manuscript and send it to a journal. Editors forward the submitted manuscripts to at least two external referees who have expertise in the topic. These reviewers can suggest the manuscript be rejected, published as is, or sent back to the scientists for more experiments. That process is called “peer review.”

Research published in peer-reviewed journals has undergone rigorous quality control by experts. Each year, about 2,800 peer-reviewed journals publish roughly 1.8 million scientific papers. The body of scientific knowledge is constantly evolving and updating, but you can trust that the science these journals describe is sound. Retraction policies help correct the record if mistakes are discovered post-publication.

Peer review takes months. To get the word out faster, scientists sometimes post research papers on what’s called a preprint server. These often have “RXiv” – pronounced “archive” – in their name: MedRXiv, BioRXiv and so on. These articles have not been peer-reviewed and so are not validated by other scientists. Preprints provide an opportunity for other scientists to evaluate and use the research as building blocks in their own work sooner.

How long has this work been on the preprint server? If it’s been months and it hasn’t yet been published in the peer-reviewed literature, be very skeptical. Are the scientists who submitted the preprint from a reputable institution? During the COVID-19 crisis, with researchers scrambling to understand a dangerous new virus and rushing to develop lifesaving treatments, preprint servers have been littered with immature and unproven science. Fastidious research standards have been sacrificed for speed.

A last warning: Be on the alert for research published in what are called predatory journals. They don’t peer-review manuscripts, and they charge authors a fee to publish. Papers from any of the thousands of known predatory journals should be treated with strong skepticism.

2. Be aware of your own biases.

Beware of biases in your own thinking that might predispose you to fall for a particular piece of fake science news.

People give their own memories and experiences more credence than they deserve, making it hard to accept new ideas and theories. Psychologists call this quirk the availability bias. It’s a useful built-in shortcut when you need to make quick decisions and don’t have time to critically analyze lots of data, but it messes with your fact-checking skills.

confirmation bias can be at work as well. People tend to give credence to news that fits their existing beliefs. This tendency helps climate change denialists and anti-vaccine advocates believe in their causes in spite of the scientific consensus against them.

 3. Correlation is not causation! Continue reading “Beware Fake Science News!”

Daydreaming on a Sunny Afternoon

I daydream. I always have.

When I’m traveling (oh, to be traveling again!), I like to wander around the place I’m visiting and fantasize about what it would be like to live there. I do the same thing staring out car or train windows.

I like to lie in bed when I first wake up and think about things. Sometimes I work on stories or essays, but sometimes I just think about something I’d like to do.

The main thing that actually gets me out of bed in the morning is the idea that once I’ve washed my face (and such) and fed the cats and made the coffee, I can sit in a comfy chair, sip my coffee, and think.

Truth be told, I think my whole life is a constant search for time to just sit and think.

So when I read this report about a scientific study that suggests most people don’t like to be alone with their thoughts, I was, to put it mildly, shocked. Especially when they reported that 67 percent of men and 25 percent of women would rather give themselves electric shocks than be alone with their thoughts.

Apparently the thing that I want most in life is anathema to a lot of people. Continue reading “Daydreaming on a Sunny Afternoon”

Half Way Across the River Jordan

I didn’t get to wear my “Not Throwing Away My Shot” hoodie to be vaccinated because the sleeves are too tight to roll up.

… or something like that. By which I mean that I have had my first dose of the two-dose COVID vaccine, which gives me the dim but hopeful feeling that there is a future out there.

I was impressed with the speed and efficiency with which my health care provider (UCSF) managed the whole thing: found an appointment on line, finished a couple of pre-visit questionnaires and the inevitable boring stuff about insurance (even if the vaccine is provided free, they may charge to administer it), and on the day of all I had to do was show up with ID and wait in line for ten minutes.  The nurse administering the shot was a pro, and the needle very fine, so the shot itself was negligible. The site itched a bit and was sore for about 24 hours–I’ve had allergy shots that were worse.

Now all I have to do is schedule the second shot, Continue reading “Half Way Across the River Jordan”

We Are Stardust

The Antennae Galaxies in Collision
The Antennae Galaxies in Collision from NASA’s Astronomy Picture of the Day

We subscribe to New Scientist, the British science magazine that provides short reports on newsworthy bits of research worldwide, several excellent columnists, and a couple of deep dives into important topics each week.

Reading each issue will remind you that our Earth is complex and interconnected and that we human beings have not come close to knowing everything there is to know about the place or, indeed, about ourselves.

Likewise, each issue will make it clear that the Universe is so vast as to be far beyond our comprehension and knowledge, at least now. We have only bits of knowledge about our little solar system, much less the Milky Way galaxy in which we reside, and both those are small potatoes within the Universe as a whole.

I also practice meditation. Of late, I’ve been meditating in the way taught by Master Li Junfeng of Sheng Zhen, which translates as the path of unconditional love, and am currently taking an online class from him to learn a form known as Heaven Earth Heart Contemplation.

When we meditate, we draw on the Earth and the Universe. As I start, I often think of the Earth – its molten core, the tectonic plates, everything from mountains to deserts to wetlands, the oceans and all the creatures – and then go out toward the Universe until I feel that I am one with the Universe.

And at the same time, I feel like I am a tiny speck in that Universe, that even the Earth is a tiny speck in it. Oddly, I find this very comforting. All those things we take so very seriously – even those on the level of life and death – don’t matter so much when I feel like this tiny bit of stardust.

That is, I come to the same place from both meditation and thinking about physics. Continue reading “We Are Stardust”

Calculating…

Every day we do risk-reward calculations: Can I cross against the light without getting hit by a car? Can I put off this task until tomorrow without getting slammed into oblivion at work? Should I have that third glass of wine? Should I get vaccinated against COVID-19 when a vaccine becomes available?

The imminent arrival of a COVID-19 vaccine (or several COVID vaccines) has brought out anti-vaccination rhetoric again, and it just… flummoxes me. The arguments I hear seem to me to be (to put it most kindly) not fully thought through. Let’s look:

Continue reading “Calculating…”